Ligand profile

PQE

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3681 — rhomboid family protease GlpG

Via homolog PDB 2nr9 UniProt P44783 Formula C₂₉H₆₀O₈
Mol. weight 536.79 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PQE
PDB
2nr9
UniProt (similar protein)
P44783
Target protein
VK055_3681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 536.79 Da
LogP (Crippen) 5.19
H-bond donors 1
H-bond acceptors 8
TPSA 84.84 Ų
Rotatable bonds 34
Aromatic rings 0 / 0
Heavy atoms 37
Fraction sp³ C 1.00
Formula C₂₉H₆₀O₈

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 84.8
  • −1 ≤ LogP ≤ 5 5.19
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 536.8
  • LogP ≤ 5 5.19
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 34
  • TPSA ≤ 140 Ų 84.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCOCCOCCOCCOCCOCCCCCOCCOCCO
InChI 
InChI=1S/C29H60O8/c1-2-3-4-5-6-7-8-9-10-12-16-31-21-24-35-26-28-37-29-27-36-25-22-33-18-14-11-13-17-32-20-23-34-19-15-30/h30H,2-29H2,1H3
InChIKey 
GEEFJAPPTAALTR-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01694

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3681.

PDB 8

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)